2-118118540-G-T

Variant names:

• chr2-118118540-G-T
• rs11673900

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.144 in 152,182 control chromosomes in the GnomAD database, including 1,624 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21945 AN: 152064 Hom.: 1620 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21967 AN: 152182 Hom.: 1624 Cov.: 32 AF XY: 0.139 AC XY: 10331 AN XY: 74422

African (AFR) AF: 0.163 AC: 6765 AN: 41508

American (AMR) AF: 0.117 AC: 1784 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 484 AN: 3464

East Asian (EAS) AF: 0.110 AC: 568 AN: 5174

South Asian (SAS) AF: 0.142 AC: 687 AN: 4824

European-Finnish (FIN) AF: 0.0812 AC: 861 AN: 10608

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.154 AC: 10452 AN: 67990

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.143 Hom.: 2905

Bravo AF: 0.147

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.93
DANN	Benign	0.52
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11673900; hg19: chr2-118876116;